Version 2.76

Term Description

SARS coronavirus 2 (SARS-CoV-2) lineage result based on a sequencing study. Results may be determined using the Pangolin lineage assignment application [https://cov-lineages.org/pangolin.html].
Source: Regenstrief LOINC

Part Descriptions

LP150045-5   Sequencing
Sequencing is a method used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes or entire genomes. Historically, most sequencing has been performed using the chain termination method developed by Frederick Sanger in 1977. PMID: 271968 Sequencing technologies have improved dramatically, making them cheaper, faster, and more accurate. Next-generation sequencing (NGS), also known as high-throughput sequencing, deep sequencing, and second-generation sequencing, is a type of technology that uses parallel sequencing of multiple small fragments of DNA to determine sequence. This "high-throughput" technology has increased the speed and amount of DNA sequenced at a significantly reduced cost. PMID: 18576944 Several NGS platforms (ie, sequencing instruments and associated reagents) have been developed. Third-generation sequencing is another methodology currently under development that uses parallel sequencing similar to NGS. In contrast to NGS, third-generation sequencing uses single DNA molecules rather than amplified DNA as a template. PMID: 20858600 Source: Regenstrief LOINC

LP422739-5   SARS coronavirus 2 lineage
Lineage nomenclatures are intended to provide a detailed level differentiation of viral mutations of SARS-CoV-2 over time. However, proposed lineage nomenclatures are not intended to portray every evolutionary change, but rather those associated with important epidemiological and biological events. PMID: 32669681 That being said they are not as broad-brushed as clades, but are expected to correspond to outbreaks. PMID: 32794443 Source: Regenstrief LOINC

Fully-Specified Name

Component
SARS coronavirus 2 lineage
Property
Type
Time
Pt
System
XXX
Scale
Nom
Method
Sequencing

Additional Names

Short Name
SARS-CoV-2 lineage Spec Seq
Display Name
SARS-CoV-2 (COVID-19) lineage Sequencing Nom (Specimen)
Consumer Name Alpha Get Info
SARS-CoV-2 (COVID-19) lineage, Specimen

Example Answer List: LL5807-4

Source: LOINC
Answer Code Score Answer ID
SARS-CoV-2 A.1.1 lineage LA31701-8
SARS-CoV-2 B.1.1.238 lineage

Also known as Nigerian variant

 LA31620-0
SARS-CoV-2 B.1.2 lineage LA31703-4
SARS-CoV-2 B.1.1 lineage LA31704-2
SARS-CoV-2 B.1.1.7 lineage

Also known as WHO Alpha variant, and UK variant

 LA31705-9
SARS-CoV-2 B.1.29 lineage LA31706-7
SARS-CoV-2 B.2.4 lineage LA31702-6
SARS-CoV-2 B.1.351 lineage

Also known as WHO Beta variant, GH/501Y.V2, and South Africa variant

 LA32553-2
SARS-CoV-2 P.1 lineage

Also known as WHO gamma lineage, and Brazil variant

 LA32555-7
SARS-CoV-2 B.1.617.2 lineage

Also known as WHO Delta variant

 LA32556-5

Basic Attributes

Class
MICRO
Type
Laboratory
First Released
Version 2.72
Last Updated
Version 2.72
Order vs. Observation
Both

Member of these Groups Get Info

LOINC Group Group Name
LG51017-8 SARSCoV2 detection
LG51019-4 SARSCoV2 molecular detection

Language Variants Get Info

Tag Language Translation
de-DE German (Germany) SARS-Coronavirus 2 Abstammungslinie:Typ:Zeitpunkt:XXX:Nominal:Sequenzierung
es-ES Spanish (Spain) Linaje de SARS-CoV-2 (COVID-19):Tipo:Punto temporal:XXX:Nom:Secuenciación
fr-FR French (France) Coronavirus SARS-CoV-2 lignée:Type:Ponctuel:Milieux divers:Résultat nominal:Séquençage
it-IT Italian (Italy) SARS coronavirus 2, lignaggio:Tipo:Pt:XXX:Nom:Sequenziamento
Synonyms: Coronavirus della SARS Lignaggio di SARS-CoV-2 (COVID-19) Microbiologia Punto nel tempo (episodio) SARS-CoV-2 (COVID-19)
nl-NL Dutch (Netherlands) SARS-CoV-2 lineage:type:moment:XXX:nominaal:sequencing
Synonyms: SARS-virus severe acute respiratory syndrome coronavirus 2; 2019-nCoV; 2019 novel coronavirus; COVID-19
pl-PL Polish (Poland) Linia rodowodowa SARS-CoV-2:typ:punkt w czasie:XXX:cecha:sekwencjonowanie
Synonyms: Koronawirus
zh-CN Chinese (China) SARS 冠状病毒 2 谱系:类型:时间点:XXX:名义型:序列测定
Synonyms: 2019 新型冠状病毒;2019 年新型冠状病毒;2019-nCoV;SARS-CoV-2;新型冠状病毒肺炎;新冠肺炎;Coronavirus disease 2019;COVID-19;冠状病毒疾病2019;严重急性呼吸综合征;severe acute respiratory syndrome;SARS;传染性非典型肺炎;infectious atypical pneumonia;非典 Ⅱ II SARS 冠状病毒 2 谱系（世系、血统、宗系、家系、种系）;2019 新型冠状病毒;2019 年新型冠状病毒;2019-nCoV;SARS-CoV-2;新型冠状病毒肺炎;新冠肺炎;Coronavirus disease 2019;COVID-19;冠状病毒疾病2019;严重急性呼吸综合征;severe acute respiratory syndrome;SARS;传染性非典型肺炎;infectious atypical pneumonia;非典 SARS;SARS 病毒;SARS-CoV;严重急性呼吸综合征;严重急性呼吸综合征病毒;萨斯病毒;非典;非典型肺炎;非典型肺炎病毒;非典病毒 不明的;其他;将在相应消息内其他部分之中加以详细说明;未作详细说明的;未作说明的;未做说明的标本;未加规定的;未加说明的标本;杂项 分类型应答;分类型结果;名义性;名称型;名词型;名词性;标称性;没有自然次序的名义型或分类型应答 型 序列分析;测序 微生物学;微生物学试验;微生物学试验（培养、DNA、抗原及抗体） 时刻;随机;随意;瞬间

LOINC Terminology Service (API) using HL7® FHIR® Get Info

CodeSystem lookup
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=100157-7